chr11-81232926-T-A

Variant names:

• chr11-81232926-T-A
• rs4943819
• ENST00000671134.1:n.324-41950T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000671134.1(ENSG00000287912):​n.324-41950T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,514 control chromosomes in the GnomAD database, including 23,198 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (23198 hom., cov: 32)
• Consequence: ENSG00000287912 ENST00000671134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 1 publications found

Genes affected

ENSG00000287912 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287912	ENST00000671134.1		n.324-41950T>A		intron	N/A
	ENSG00000287912	ENST00000671210.1		n.310-41950T>A		intron	N/A
	ENSG00000287912	ENST00000701193.2		n.196-41950T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79540 AN: 151396 Hom.: 23141 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.541

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.526 AC: 79654 AN: 151514 Hom.: 23198 Cov.: 32 AF XY: 0.527 AC XY: 38975 AN XY: 74024

African (AFR) AF: 0.734 AC: 30388 AN: 41402

American (AMR) AF: 0.586 AC: 8896 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1546 AN: 3460

East Asian (EAS) AF: 0.937 AC: 4827 AN: 5150

South Asian (SAS) AF: 0.476 AC: 2290 AN: 4814

European-Finnish (FIN) AF: 0.356 AC: 3753 AN: 10548

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26434 AN: 67656

Other (OTH) AF: 0.546 AC: 1146 AN: 2100

Alfa AF: 0.470 Hom.: 2273

Bravo AF: 0.556

Asia WGS AF: 0.739 AC: 2554 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.26
PhyloP100		0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4943819; hg19: chr11-80943969;